Variant 1-15443607-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_007272.3(CTRC):c.493+52G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0977 in 1,611,828 control chromosomes in the GnomAD database, including 8,190 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 906 hom., cov: 32)

Exomes 𝑓: 0.097 ( 7284 hom. )

Consequence

CTRC
NM_007272.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.694

Variant links:

Genes affected

CTRC (HGNC:2523): (chymotrypsin C) This gene encodes a member of the peptidase S1 family. The encoded protein is a serum calcium-decreasing factor that has chymotrypsin-like protease activity. Alternatively spliced transcript variants have been observed, but their full-length nature has not been determined. [provided by RefSeq, Jul 2008]

CTRC links:

CTRC (HGNC:):

CTRC links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 1-15443607-G-A is Benign according to our data. Variant chr1-15443607-G-A is described in ClinVar as [Benign]. Clinvar id is 439564.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CTRC	NM_007272.3 linkuse as main transcript	c.493+52G>A		intron_variant		ENST00000375949.5	NP_009203.2	Q99895
CTRC	XM_011540550.2 linkuse as main transcript	c.493+52G>A		intron_variant			XP_011538852.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
CTRC	ENST00000375949.5 linkuse as main transcript	c.493+52G>A	intron_variant	1	NM_007272.3	ENSP00000365116.4	Q99895
CTRC	ENST00000375943.6 linkuse as main transcript	c.*93+52G>A	intron_variant	1		ENSP00000365110.2	Q68DR9
CTRC	ENST00000483406.1 linkuse as main transcript	n.403+52G>A	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.106

AC:

16097

AN:

152178

Hom.:

904

Cov.:

show subpopulations

Gnomad AFR

AF:

0.128

Gnomad AMI

AF:

0.0943

Gnomad AMR

AF:

0.0838

Gnomad ASJ

AF:

0.103

Gnomad EAS

AF:

0.00384

Gnomad SAS

AF:

0.0687

Gnomad FIN

AF:

0.113

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.107

Gnomad OTH

AF:

0.114

GnomAD3 exomes

AF:

0.0891

AC:

22330

AN:

250700

Hom.:

1098

AF XY:

0.0894

AC XY:

12123

AN XY:

135584

show subpopulations

Gnomad AFR exome

AF:

0.126

Gnomad AMR exome

AF:

0.0545

Gnomad ASJ exome

AF:

0.122

Gnomad EAS exome

AF:

0.00299

Gnomad SAS exome

AF:

0.0781

Gnomad FIN exome

AF:

0.110

Gnomad NFE exome

AF:

0.104

Gnomad OTH exome

AF:

0.0947

GnomAD4 exome

AF:

0.0969

AC:

141370

AN:

1459532

Hom.:

7284

Cov.:

AF XY:

0.0964

AC XY:

69989

AN XY:

726234

show subpopulations

Gnomad4 AFR exome

AF:

0.127

Gnomad4 AMR exome

AF:

0.0574

Gnomad4 ASJ exome

AF:

0.116

Gnomad4 EAS exome

AF:

0.00176

Gnomad4 SAS exome

AF:

0.0763

Gnomad4 FIN exome

AF:

0.112

Gnomad4 NFE exome

AF:

0.102

Gnomad4 OTH exome

AF:

0.0929

GnomAD4 genome

AF:

0.106

AC:

16109

AN:

152296

Hom.:

906

Cov.:

AF XY:

0.105

AC XY:

7783

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.127

Gnomad4 AMR

AF:

0.0836

Gnomad4 ASJ

AF:

0.103

Gnomad4 EAS

AF:

0.00385

Gnomad4 SAS

AF:

0.0689

Gnomad4 FIN

AF:

0.113

Gnomad4 NFE

AF:

0.107

Gnomad4 OTH

AF:

0.115

Alfa

AF:

0.107

Hom.:

209

Bravo

AF:

0.105

Asia WGS

AF:

0.0620

AC:

215

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 21, 2018	- -

Hereditary pancreatitis

Benign:1

Benign, criteria provided, single submitter

clinical testing

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Feb 28, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.014

DANN

Benign

0.51

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over